Contacts of the helix formed by residues 189 - 206 (chain I) in PDB entry 5D3E
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 189 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183I TYR* 2.9 16.7 + - + +
184I TYR 4.1 0.6 + - - -
187I GLN* 3.9 13.9 - - + +
188I ASN* 1.3 76.4 - - - +
190I PRO* 1.3 66.9 - - - +
191I GLU* 3.1 15.4 + - - +
192I GLN* 3.1 29.5 + - + +
193I ALA* 3.2 11.4 + - - +
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Residues in contact with PRO 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184I TYR* 3.8 35.4 - - + +
188I ASN* 3.5 12.8 - - - +
189I ALA* 1.3 87.5 - - - +
191I GLU* 1.3 69.7 - - + +
193I ALA* 3.7 1.5 - - + +
194I CYS* 2.9 40.8 + - - -
233I TRP 5.6 3.1 - - - +
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Residues in contact with GLU 191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189I ALA* 3.1 20.6 + - - +
190I PRO* 1.3 90.0 - - + +
192I GLN* 1.3 61.9 + - + +
194I CYS* 3.9 3.5 - - - +
195I HIS* 2.9 29.8 + - - +
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Residues in contact with GLN 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183I TYR* 2.9 45.6 + - + -
189I ALA* 3.1 18.1 + - + +
191I GLU* 1.3 84.3 - - + +
193I ALA* 1.3 58.5 + - - +
195I HIS* 3.6 7.4 - - - +
196I LEU* 2.9 30.3 + - - +
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Residues in contact with ALA 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180I SER* 3.3 34.1 - - - +
183I TYR* 3.7 8.9 - - + +
184I TYR* 3.6 19.7 - - + +
189I ALA 3.2 8.0 + - - +
190I PRO* 3.7 8.5 - - + +
191I GLU 3.2 0.2 - - - -
192I GLN* 1.3 74.7 - - - +
194I CYS* 1.3 64.1 + - - +
196I LEU 3.5 0.3 + - - -
197I ALA* 3.1 24.6 + - - +
233I TRP* 3.8 14.7 - - + -
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Residues in contact with CYS 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190I PRO* 2.9 29.0 + - - +
191I GLU* 3.9 3.8 - - - +
193I ALA* 1.3 74.6 - - - +
195I HIS* 1.3 59.6 + - - +
198I LYS* 2.8 34.9 + - + +
230I LEU* 3.6 24.1 - - + +
233I TRP* 4.0 31.2 - - - -
234I THR* 4.6 15.0 - - + -
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Residues in contact with HIS 195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191I GLU 2.9 18.6 + - - +
192I GLN* 3.6 8.7 + - - +
194I CYS* 1.3 77.9 - - - +
196I LEU* 1.3 57.8 + - - +
198I LYS* 4.3 3.9 - - - +
199I THR* 2.5 55.2 + - + -
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Residues in contact with LEU 196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158I HIS* 3.8 30.3 - - + +
162I LYS* 5.9 1.1 - - - +
176I ALA* 4.4 17.5 - - + +
179I TYR* 3.5 42.2 - - + -
180I SER* 4.2 5.4 - - - +
183I TYR* 3.9 20.0 - - + -
192I GLN 2.9 16.8 + - - +
193I ALA 4.0 3.6 - - - +
195I HIS* 1.3 80.1 + - - +
197I ALA* 1.3 62.6 + - - +
198I LYS 3.4 0.2 - - - -
199I THR* 4.0 5.3 - - + -
200I ALA* 3.2 22.1 + - + +
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Residues in contact with ALA 197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176I ALA 5.3 0.4 - - - -
180I SER* 4.1 12.5 - - - +
193I ALA 3.1 17.2 + - - +
194I CYS 3.9 2.7 - - - +
196I LEU* 1.3 78.2 - - - +
198I LYS* 1.3 59.7 + - - +
200I ALA* 3.9 0.2 - - - +
201I PHE* 3.0 28.4 + - - +
226I LEU* 3.7 31.1 - - + +
229I ASN* 6.1 0.9 - - + -
230I LEU* 4.0 21.1 - - + +
233I TRP* 4.6 5.4 - - + -
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Residues in contact with LYS 198 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194I CYS* 2.8 17.6 + - + +
195I HIS* 4.3 3.8 - - - +
197I ALA* 1.3 75.8 - - - +
199I THR* 1.3 56.8 + - - +
201I PHE* 3.2 3.6 + - + +
202I ASP* 2.7 69.1 + - - +
230I LEU* 3.8 20.3 - - + +
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Residues in contact with THR 199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162I LYS* 4.1 20.4 - - - +
195I HIS* 2.5 42.5 + - + -
196I LEU* 4.0 8.1 - - + -
198I LYS* 1.3 79.0 - - - +
200I ALA* 1.3 57.1 + - - +
202I ASP* 3.8 5.1 - - - +
203I ASP* 3.0 53.2 + - - +
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Residues in contact with ALA 200 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167I PRO* 4.6 1.4 - - - +
173I LEU* 4.0 10.1 - - + +
176I ALA* 3.4 29.4 - - + -
196I LEU* 3.2 19.8 + - + +
197I ALA* 3.9 4.7 - - - +
198I LYS 3.2 0.4 - - - -
199I THR* 1.3 76.6 - - - +
201I PHE* 1.3 64.9 + - - +
203I ASP* 3.8 5.5 + - - +
204I ALA* 3.3 22.2 + - - +
226I LEU* 4.7 5.8 - - + -
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Residues in contact with PHE 201 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173I LEU* 5.4 0.4 - - - -
197I ALA 3.0 19.5 + - - +
198I LYS* 3.6 5.8 - - + +
200I ALA* 1.3 75.0 - - - +
202I ASP* 1.3 80.2 + - - +
204I ALA* 3.2 6.7 + - - +
205I ILE* 3.0 45.2 + - + +
223I MET* 3.7 45.3 - - + -
226I LEU* 4.6 12.9 - - + +
227I ARG* 3.6 47.1 - - + -
230I LEU* 5.0 5.2 - - + -
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Residues in contact with ASP 202 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198I LYS* 2.7 56.7 + - - +
199I THR* 3.8 5.8 + - - +
201I PHE* 1.3 87.5 - - - +
203I ASP* 1.3 61.2 + - - +
205I ILE* 2.9 22.4 + - - +
206I ALA* 2.9 16.4 + - - +
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Residues in contact with ASP 203 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162I LYS* 4.5 5.9 + - - -
167I PRO* 3.5 27.3 - - + +
172I ARG* 4.3 13.8 + - - +
199I THR* 3.0 37.1 + - - +
200I ALA* 4.1 5.0 - - - +
202I ASP* 1.3 78.1 - - - +
204I ALA* 1.3 60.6 - - - +
206I ALA* 3.8 6.5 + - - +
207I GLU* 3.8 17.8 + - - +
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Residues in contact with ALA 204 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167I PRO* 3.4 25.7 - - - +
168I THR* 3.5 15.6 - - + +
173I LEU* 3.9 11.7 - - + -
200I ALA 3.3 14.5 + - - +
201I PHE 3.2 6.3 + - - +
203I ASP* 1.3 78.1 - - - +
205I ILE* 1.3 62.8 + - - +
207I GLU 3.3 4.2 + - - -
208I LEU* 3.2 21.3 + - - +
223I MET* 4.0 17.9 - - + -
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Residues in contact with ILE 205 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201I PHE* 3.0 42.5 + - + +
202I ASP* 2.9 12.4 + - - +
204I ALA* 1.3 72.0 - - - +
206I ALA* 1.3 60.1 + - - +
207I GLU 2.9 10.7 + - - -
208I LEU* 2.9 40.6 + - + +
223I MET* 3.5 20.6 - - + -
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Residues in contact with ALA 206 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202I ASP 2.9 14.2 + - - +
203I ASP* 4.0 9.4 - - - +
205I ILE* 1.3 77.8 - - - +
207I GLU* 1.3 65.9 + - + +
208I LEU 3.6 0.8 + - - -
209I ASP* 4.3 5.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il